This notebook will begin looking at clustering methods on the expression of the genes in a single sample of the dataset of interest, from an unbiased approach.

Set Up

# Load libraries
library(magrittr)
library(scater)
library(readr)
library(bluster)
library(ggpubr)
library(pheatmap)

# Set file paths
data_dir <- file.path("results", "Gawad_processed_data")

# Source custom functions script
source(file.path("utils", "clustering-functions.R"))

Read in data

sample_290_normalized <- read_rds(
  file.path(data_dir, "SCPCS000216", "SCPCL000290_miQC_downstream_processed_normalized_reduced_sce.rds"))

Perform clustering

k-means

# Perform k-means clustering
sample_290_normalized <- kmeans_clustering(
  sample_290_normalized,
  params_range = c(4:10),
  step_size = 1,
  check_stability = TRUE
)

# grab column names with clustering results
kmeans_cols <- grep("kmeans", colnames(colData(sample_290_normalized)))
kmeans_cluster_names <- colnames(colData(sample_290_normalized)[, kmeans_cols])

# Plot k-means
kmeans_plot_list <- kmeans_cluster_names %>%
  purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + 
               theme_bw()+
               theme(text = element_text(size = 22)))

cowplot::plot_grid(plotlist = kmeans_plot_list, ncol = 4)

graph-based, walktrap

# Perform graph-based walktrap clustering
sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  params_range = c(5:25),
  step_size = 5,
  weighting_type = "rank",
  cluster_function = "walktrap",
  check_stability = TRUE
)
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# grab column names with clustering results
walktrap_cols <- grep("walktrap", colnames(colData(sample_290_normalized)))
walktrap_cluster_names <- colnames(colData(sample_290_normalized)[, walktrap_cols])

# Plot
walktrap_plot_list <- walktrap_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + 
                theme_bw() +
                theme(text = element_text(size = 22)))

cowplot::plot_grid(plotlist = walktrap_plot_list, ncol = 3)

graph-based, louvain

# Perform graph-based louvain clustering
sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  params_range = c(5:25),
  step_size = 5,
  weighting_type = "jaccard",
  cluster_function = "louvain",
  check_stability = TRUE
)
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# grab column names with clustering results
louvain_cols <- grep("walktrap", colnames(colData(sample_290_normalized)))
louvain_cluster_names <- colnames(colData(sample_290_normalized)[, louvain_cols])

# Plot
louvain_plot_list <- louvain_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + 
                theme_bw() +
                theme(text = element_text(size = 22)))


cowplot::plot_grid(plotlist = louvain_plot_list, ncol = 3)

Check cluster validity stats

k-means

# Check the k-means cluster validity stats for each of the clusters and return
# stats in a data frame
kmeans_stats_df <- create_metadata_stats_df(sample_290_normalized, c(4:10), 1, "kmeans")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the results
head(kmeans_stats_df)

# Summarize the stats and return in a data frame
kmeans_summary_stats_df <- summarize_clustering_stats(kmeans_stats_df)
`summarise()` has grouped output by 'cluster_names_column', 'cluster_type'. You can override using the `.groups` argument.
# Preview the summary results
head(kmeans_summary_stats_df)

purity plots

# Plot individual cluster purity stats
kmeans_purity_plots <- plot_cluster_purity(kmeans_stats_df)

kmeans_purity_plots

silhouette width plots

# Plot individual cluster silhouette width stats
kmeans_silhouette_plots <- plot_cluster_silhouette_width(kmeans_stats_df)

kmeans_silhouette_plots

graph-based, walktrap

# Check the walktrap cluster validity stats for each of the clusters and return
# stats in a data frame
walktrap_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "walktrap")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
  
# Preview the all stats results
head(walktrap_stats_df)

# Summarize the stats and return in a data frame
walktrap_summary_stats_df <- summarize_clustering_stats(walktrap_stats_df)
`summarise()` has grouped output by 'cluster_names_column', 'cluster_type'. You can override using the `.groups` argument.
# Preview the summary results
head(walktrap_summary_stats_df)

purity plots

# Plot individual cluster purity stats
walktrap_purity_plots <- plot_cluster_purity(walktrap_stats_df)

walktrap_purity_plots

silhouette width plots

# Plot individual cluster silhouette width stats
walktrap_silhouette_plots <- plot_cluster_silhouette_width(walktrap_stats_df)

walktrap_silhouette_plots

graph-based, louvain

# Check the louvain cluster validity stats for each of the clusters and return
# stats in a data frame
louvain_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "louvain")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the results
head(louvain_stats_df)

# Summarize the stats and return in a data frame
louvain_summary_stats_df <- summarize_clustering_stats(louvain_stats_df)
`summarise()` has grouped output by 'cluster_names_column', 'cluster_type'. You can override using the `.groups` argument.
# Preview the summary results
head(louvain_summary_stats_df)

purity plots

# Plot individual cluster purity stats
louvain_purity_plots <- plot_cluster_purity(louvain_stats_df)

louvain_purity_plots

silhouette width plots

# Plot individual cluster silhouette width stats
louvain_silhouette_plots <- plot_cluster_silhouette_width(louvain_stats_df)

louvain_silhouette_plots

Summary plots

summary_stats_df_list <- list("walktrap" = walktrap_summary_stats_df,
                              "louvain" = louvain_summary_stats_df)

# purity summary plot
plot_avg_validity_stats(summary_stats_df_list, "avg_purity")


#silhouette width summary plot
plot_avg_validity_stats(summary_stats_df_list, "avg_width")

Check cluster stability

k-means

# Check cluster stability
kmeans_bootstrapping_df <- plot_cluster_stability(sample_290_normalized, c(4:10), 1, "kmeans")
kmeans_bootstrapping_df
$bootstrapping_results_kmeans_4
          1         2         3         4
1 0.9670238 0.9809463 0.9486430 0.9660998
2        NA 0.9482672 0.9285272 0.9357409
3        NA        NA 0.9350124 0.9835877
4        NA        NA        NA 1.0055630

$bootstrapping_results_kmeans_5
          1         2         3         4         5
1 0.9995784 0.9926340 0.9986594 0.9980652 0.9984129
2        NA 0.9299901 0.8933558 0.9979998 0.9485987
3        NA        NA 0.9308782 0.9977533 0.8601109
4        NA        NA        NA 0.9668614 0.9674479
5        NA        NA        NA        NA 0.8866566

$bootstrapping_results_kmeans_6
         1         2         3         4         5         6
1 1.001477 0.9985228 0.9985228 0.9985228 0.9985228 0.9914215
2       NA 0.9044500 0.8570454 0.9838284 0.8649372 0.8224922
3       NA        NA 0.8759325 0.9900975 0.7858050 0.9895819
4       NA        NA        NA 0.8792771 0.8181676 0.9725378
5       NA        NA        NA        NA 0.6785048 0.9405953
6       NA        NA        NA        NA        NA 0.8975756

$bootstrapping_results_kmeans_7
          1         2         3         4          5         6         7
1 0.9001054 1.0998946 1.0998946 1.0998946  1.0998946 1.0976913 1.0998946
2        NA 0.4188519 0.4037244 1.0347909 -2.2723041 1.0388735 0.7674261
3        NA        NA 0.7258064 1.0043798  1.0202658 1.0844502 0.8066779
4        NA        NA        NA 0.5423137  1.0363891 1.0763617 0.5390403
5        NA        NA        NA        NA  0.6468716 0.7545548 0.9541823
6        NA        NA        NA        NA         NA 0.7590055 0.9883267
7        NA        NA        NA        NA         NA        NA 0.3290688

$bootstrapping_results_kmeans_8
          1         2         3         4         5         6         7         8
1 0.9901963 1.0075234 1.0075234 1.0075234 1.0075234 1.0051596 1.0075234 1.0075234
2        NA 0.7813833 0.7230846 0.8175508 0.4452037 0.9754934 0.7980177 1.0073305
3        NA        NA 0.8575095 0.8887555 0.9617900 1.0009774 0.9882169 1.0074675
4        NA        NA        NA 0.8459702 0.9770733 0.9961512 0.7594789 0.8039574
5        NA        NA        NA        NA 0.9299259 0.8926684 1.0045905 1.0038561
6        NA        NA        NA        NA        NA 0.8729004 0.9552194 0.9930871
7        NA        NA        NA        NA        NA        NA 0.7744634 1.0041145
8        NA        NA        NA        NA        NA        NA        NA 0.9614452

$bootstrapping_results_kmeans_9
          1         2         3         4          5         6         7         8          9
1 0.9332904 1.0650353 1.0650353 1.0650353  1.0650353 1.0382998 1.0650353 1.0650353  1.0650353
2        NA 0.1964553 0.1526277 0.1372241 -0.9438084 0.9912888 0.8278951 1.0578945 -0.8687848
3        NA        NA 0.8274036 0.8497683  0.7745327 1.0375410 0.9777208 1.0650353  1.0062683
4        NA        NA        NA 0.7540287  1.0142023 1.0264148 0.7062673 0.6914737  1.0381503
5        NA        NA        NA        NA  0.5562033 0.9950810 0.6247015 1.0650353  0.2076352
6        NA        NA        NA        NA         NA 0.7694919 0.9935326 1.0191571  0.7987781
7        NA        NA        NA        NA         NA        NA 0.6731171 1.0650353  1.0636731
8        NA        NA        NA        NA         NA        NA        NA 0.9295724  1.0650353
9        NA        NA        NA        NA         NA        NA        NA        NA  0.6077338

$bootstrapping_results_kmeans_10
           1         2         3         4          5         6         7          8         9
1  0.9901451 0.9956219 0.9956219 0.9956219  0.9956219 0.9831498 0.9953332  0.9956219 0.9956219
2         NA 0.6166200 0.9829807 0.9956219 -0.2422819 0.9188056 0.7776176  0.9841653 0.2180217
3         NA        NA 0.8035013 0.9927305  0.9888109 0.0190354 0.9956219  0.9610742 0.8255615
4         NA        NA        NA 0.9931459  0.9956219 0.9927305 0.9956219  0.4488661 0.9956219
5         NA        NA        NA        NA  0.2643743 0.9806301 0.6084785 -0.5511335 0.3906408
6         NA        NA        NA        NA         NA 0.7550918 0.9591186  0.9927305 0.8492959
7         NA        NA        NA        NA         NA        NA 0.8104246  0.8966279 0.9937464
8         NA        NA        NA        NA         NA        NA        NA  0.7326773 0.9924650
9         NA        NA        NA        NA         NA        NA        NA         NA 0.6022141
10        NA        NA        NA        NA         NA        NA        NA         NA        NA
          10
1  0.9956219
2  0.7472531
3  0.9690572
4  0.9956219
5  0.1587312
6  0.9850445
7  0.9846398
8  0.9744221
9  0.8250984
10 0.7981454

graph-based, walktrap

walktrap_bootstrapping_df <- plot_cluster_stability(sample_290_normalized, c(5:25), 5, "walktrap")
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
walktrap_bootstrapping_df
$bootstrapping_results_walktrap_5
           1         2           3         4         5         6         7          8           9
1  0.2337592 0.3641509  0.69503233 0.4863197 0.7962920 0.7881401 0.7962920 -0.1400388  0.70287500
2         NA 0.2057748 -0.02691831 0.3544477 0.7791915 0.7285337 0.7664118  0.4100090  0.08976628
3         NA        NA  0.47237401 0.6773503 0.7962920 0.7906039 0.7900004  0.7723067  0.61767860
4         NA        NA          NA 0.1722388 0.7962920 0.7778429 0.7807839  0.5895016  0.49057258
5         NA        NA          NA        NA 0.4765148 0.7807839 0.7962920  0.7407085  0.79629202
6         NA        NA          NA        NA        NA 0.4226707 0.7962920  0.7165692  0.78031876
7         NA        NA          NA        NA        NA        NA 0.5418302  0.7962920 -0.12936736
8         NA        NA          NA        NA        NA        NA        NA  0.2583178  0.73789757
9         NA        NA          NA        NA        NA        NA        NA         NA  0.39532372
10        NA        NA          NA        NA        NA        NA        NA         NA          NA
11        NA        NA          NA        NA        NA        NA        NA         NA          NA
12        NA        NA          NA        NA        NA        NA        NA         NA          NA
13        NA        NA          NA        NA        NA        NA        NA         NA          NA
14        NA        NA          NA        NA        NA        NA        NA         NA          NA
15        NA        NA          NA        NA        NA        NA        NA         NA          NA
16        NA        NA          NA        NA        NA        NA        NA         NA          NA
17        NA        NA          NA        NA        NA        NA        NA         NA          NA
18        NA        NA          NA        NA        NA        NA        NA         NA          NA
19        NA        NA          NA        NA        NA        NA        NA         NA          NA
20        NA        NA          NA        NA        NA        NA        NA         NA          NA
21        NA        NA          NA        NA        NA        NA        NA         NA          NA
22        NA        NA          NA        NA        NA        NA        NA         NA          NA
23        NA        NA          NA        NA        NA        NA        NA         NA          NA
24        NA        NA          NA        NA        NA        NA        NA         NA          NA
25        NA        NA          NA        NA        NA        NA        NA         NA          NA
26        NA        NA          NA        NA        NA        NA        NA         NA          NA
27        NA        NA          NA        NA        NA        NA        NA         NA          NA
28        NA        NA          NA        NA        NA        NA        NA         NA          NA
29        NA        NA          NA        NA        NA        NA        NA         NA          NA
30        NA        NA          NA        NA        NA        NA        NA         NA          NA
31        NA        NA          NA        NA        NA        NA        NA         NA          NA
           10          11        12            13       14        15       16        17        18
1   0.5523530  0.47172076 0.7358114  0.7158467451 0.796292 0.7962920 0.796292 0.7962920 0.4436454
2   0.3529728  0.05439643 0.7371911  0.5978696669 0.796292 0.7962920 0.796292 0.7962920 0.7807839
3   0.7465086  0.59765984 0.7667935  0.7842666957 0.796292 0.7962920 0.796292 0.7962920 0.7962920
4   0.3983402  0.55153467 0.7962920  0.7778429196 0.796292 0.7962920 0.796292 0.7962920 0.1516812
5   0.7549208  0.56599856 0.7836219 -0.0805628985 0.796292 0.7962920 0.796292 0.6972753 0.7962920
6   0.7678679  0.76786794 0.7962920  0.7678679383 0.796292 0.7962920 0.796292 0.3068858 0.7962920
7   0.7962920  0.79629202 0.7863170  0.7962920224 0.796292 0.7962920 0.796292 0.7962920 0.7962920
8  -0.1949394 -1.28922906 0.5617427 -0.0005161271 0.796292 0.7962920 0.796292 0.7807839 0.7430175
9   0.7080568  0.70232974 0.7807839  0.7747052597 0.796292 0.7962920 0.796292 0.7962920 0.7962920
10  0.4105566 -0.49938845 0.7175276  0.3770726472 0.796292 0.7962920 0.796292 0.7962920 0.6027030
11         NA  0.27937780 0.5264047 -0.8630218944 0.796292 0.7962920 0.796292 0.7962920 0.7804728
12         NA          NA 0.4919512  0.5947988904 0.796292 0.7793062 0.796292 0.7863170 0.7962920
13         NA          NA        NA  0.5193245529 0.796292 0.7962920 0.796292 0.7962920 0.7807839
14         NA          NA        NA            NA 0.720464 0.5007432 0.796292 0.7962920 0.7962920
15         NA          NA        NA            NA       NA 0.8418299 0.796292 0.7807839 0.7962920
16         NA          NA        NA            NA       NA        NA 1.156543 0.7962920 0.7962920
17         NA          NA        NA            NA       NA        NA       NA 0.7689758 0.7962920
18         NA          NA        NA            NA       NA        NA       NA        NA 0.5494790
19         NA          NA        NA            NA       NA        NA       NA        NA        NA
20         NA          NA        NA            NA       NA        NA       NA        NA        NA
21         NA          NA        NA            NA       NA        NA       NA        NA        NA
22         NA          NA        NA            NA       NA        NA       NA        NA        NA
23         NA          NA        NA            NA       NA        NA       NA        NA        NA
24         NA          NA        NA            NA       NA        NA       NA        NA        NA
25         NA          NA        NA            NA       NA        NA       NA        NA        NA
26         NA          NA        NA            NA       NA        NA       NA        NA        NA
27         NA          NA        NA            NA       NA        NA       NA        NA        NA
28         NA          NA        NA            NA       NA        NA       NA        NA        NA
29         NA          NA        NA            NA       NA        NA       NA        NA        NA
30         NA          NA        NA            NA       NA        NA       NA        NA        NA
31         NA          NA        NA            NA       NA        NA       NA        NA        NA
          19         20       21        22        23        24         25         26        27
1  0.7870546  0.7807839 0.796292 0.4678422 0.7962920 0.7807839  0.7962920  0.7962920  0.796292
2  0.7524016  0.7671681 0.796292 0.7672932 0.7962920 0.7047506  0.7962920  0.7962920  0.796292
3  0.7524913  0.7962920 0.796292 0.7962920 0.7937182 0.6476336  0.7951034  0.7807839  0.796292
4  0.7799403  0.7962920 0.796292 0.4615404 0.7962920 0.7678679  0.7962920  0.7962920  0.796292
5  0.7962920  0.7962920 0.796292 0.7962920 0.7962920 0.7962920  0.7807839  0.7962920  0.796292
6  0.7939421 -0.2509264 0.796292 0.7703470 0.7962920 0.7962920  0.7203084  0.7962920  0.796292
7  0.6090922  0.7807839 0.796292 0.7962920 0.7962920 0.7962920  0.7962920  0.7962920  0.796292
8  0.7935039  0.7651738 0.796292 0.6242991 0.7962920 0.7962920  0.7941565  0.7807839  0.796292
9  0.7719443  0.7633336 0.796292 0.7786231 0.7962920 0.7665611  0.7962920  0.7950357  0.796292
10 0.7962920  0.7962920 0.796292 0.6372916 0.7962920 0.7808165  0.7962920  0.7962920  0.796292
11 0.7888724  0.7807839 0.796292 0.7669010 0.7962920 0.7692688  0.7962920  0.7678679  0.796292
12 0.4296328  0.7962920 0.796292 0.7962920 0.7727242 0.5656045  0.7807839 -0.7390529  0.796292
13 0.7962920  0.7962920 0.796292 0.7962920 0.7962920 0.7962920  0.7962920  0.7807839  0.796292
14 0.7287345  0.7962920 0.796292 0.7962920 0.2613518 0.7962920  0.7807839  0.7962920  0.796292
15 0.7199317  0.7962920 0.796292 0.7962920 0.5943317 0.7807839  0.6389421  0.5441175  0.796292
16 0.7962920  0.7962920 0.796292 0.7962920 0.7962920 0.7962920  0.7962920  0.7962920 -2.549730
17 0.7962920  0.7574311 0.796292 0.7807839 0.7962920 0.7962920 -3.0576375  0.7863170  0.796292
18 0.7962920  0.7962920 0.796292 0.1170607 0.7962920 0.7962920  0.7962920  0.7962920  0.796292
19 0.6429076  0.7962920 0.796292 0.7962920 0.7039821 0.4120714  0.7678679  0.5616306  0.796292
20        NA  0.9129716 0.796292 0.7962920 0.7962920 0.7962920  0.7807839  0.7962920  0.796292
21        NA         NA 1.103378 0.7962920 0.7962920 0.7962920  0.7962920  0.7962920  0.796292
22        NA         NA       NA 0.4950029 0.7962920 0.7962920  0.7962920  0.7962920  0.796292
23        NA         NA       NA        NA 1.0127896 0.7807839  0.7962920  0.7952061  0.796292
24        NA         NA       NA        NA        NA 0.8697287  0.7807839  0.6332141  0.796292
25        NA         NA       NA        NA        NA        NA  1.1142243  0.7574311  0.796292
26        NA         NA       NA        NA        NA        NA         NA  0.5847220  0.796292
27        NA         NA       NA        NA        NA        NA         NA         NA  1.093363
28        NA         NA       NA        NA        NA        NA         NA         NA        NA
29        NA         NA       NA        NA        NA        NA         NA         NA        NA
30        NA         NA       NA        NA        NA        NA         NA         NA        NA
31        NA         NA       NA        NA        NA        NA         NA         NA        NA
           28         29        30       31
1   0.7962920  0.7962920 0.7962920 0.796292
2   0.7962920  0.7962920 0.7962920 0.796292
3   0.7962920  0.7962920 0.7962920 0.796292
4   0.7962920  0.7962920 0.7962920 0.796292
5   0.7962920  0.7962920 0.7962920 0.796292
6   0.7962920  0.7962920 0.7962920 0.796292
7  -0.2567903  0.7962920 0.7962920 0.796292
8   0.7962920  0.7962920 0.7962920 0.796292
9   0.7603720  0.7962920 0.7962920 0.796292
10  0.7962920  0.7962920 0.7962920 0.796292
11  0.7962920  0.7962920 0.7962920 0.796292
12  0.7962920  0.7962920 0.6405317 0.796292
13  0.7962920  0.7962920 0.7962920 0.796292
14  0.7962920  0.7962920 0.7962920 0.796292
15  0.7962920  0.7962920 0.6906954 0.796292
16  0.7962920  0.7962920 0.7962920 0.796292
17  0.7962920  0.7962920 0.7863170 0.796292
18  0.7962920  0.7962920 0.7962920 0.796292
19  0.7962920  0.7962920 0.6033720 0.796292
20  0.7962920  0.7962920 0.7962920 0.796292
21  0.7962920 -0.3747467 0.7807839 0.796292
22  0.7962920  0.7962920 0.7962920 0.796292
23  0.7962920  0.7962920 0.7962920 0.796292
24  0.7962920  0.7962920 0.6641389 0.796292
25  0.7962920  0.7962920 0.7807839 0.796292
26  0.7962920  0.7962920 0.5956118 0.796292
27  0.7962920  0.7962920 0.7962920 0.796292
28  1.1916350  0.7962920 0.7962920 0.796292
29         NA  1.1137857 0.7962920 0.796292
30         NA         NA 1.0567321 0.796292
31         NA         NA        NA 1.203708

$bootstrapping_results_walktrap_10
           1        2         3         4         5         6          7         8         9         10
1  0.7368454 1.126842 1.1266952 1.1268420 1.1251463 1.1268420  1.1267596 1.1001446 1.1268420  1.1268420
2         NA 0.586268 1.1268420 0.6168567 1.1090246 1.1268420  1.1131067 1.1067230 1.1268420  0.9333110
3         NA       NA 0.5364273 1.1068697 1.0477022 1.0560960  0.9997905 1.0133417 1.0882808  1.1268420
4         NA       NA        NA 0.6203908 1.0320946 1.0543975  1.0134269 1.1268420 1.0867558  1.1071949
5         NA       NA        NA        NA 0.3798614 1.0757234 -1.2563429 1.0155422 0.4994805  0.1295646
6         NA       NA        NA        NA        NA 0.4563509  1.0513898 1.1068351 1.0947087  1.1268420
7         NA       NA        NA        NA        NA        NA  0.2574431 1.1236753 0.2316001 -0.8266955
8         NA       NA        NA        NA        NA        NA         NA 0.6366548 1.1268420  1.1268420
9         NA       NA        NA        NA        NA        NA         NA        NA 0.3809386  1.1050585
10        NA       NA        NA        NA        NA        NA         NA        NA        NA  0.6754657
11        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
12        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
13        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
14        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
15        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
16        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
17        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
18        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
19        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
20        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
21        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
22        NA       NA        NA        NA        NA        NA         NA        NA        NA         NA
           11          12        13         14         15         16         17          18          19
1   1.1268420  1.12684196 0.5979856  1.1268420  1.1268420  1.1268420  1.1020984  1.12684196  1.12684196
2   1.1268420  1.12684196 1.1063816  1.1268420  1.0975578  1.1268420  1.1067230  1.12684196  1.12684196
3   1.1067230 -0.30037543 1.1268420  0.9168992  1.1236318  1.1268420  1.1008033  1.12388503  1.12669522
4   1.1204582  0.97467131 1.1268420  0.7918143  1.1013198  1.1235632  1.1268420  1.10014462  1.10948541
5   1.0920475  0.05869578 1.1240256  0.8640745  0.8137207  1.0729556  0.6252446  0.06583510  0.28239966
6  -0.4252930  0.72762890 1.1268420 -0.6280101  1.1268420  1.1268420  1.1131067  1.12684196  1.12684196
7   1.1190305 -0.76970745 1.1268420 -0.4677229  0.8645709  1.1127801  1.0012403 -0.01855122  0.04554126
8   1.1268420  1.11310671 0.9550913  1.1131067  1.1268420  1.1268420 -0.6351765  1.12684196  1.12684196
9   1.1268420  0.58122910 1.1268420  0.4001945 -2.3566571  0.7382732  1.1250517  0.84407500 -1.61689683
10  1.1268420  1.06308088 1.1268420  1.1131067  1.1245528  1.1268420  1.0616623  1.02146736  1.02533597
11  0.6481865  1.10493757 1.1268420  1.0014677  1.1268420  1.1268420  1.1268420  1.12684196  1.12684196
12         NA  0.40039969 1.1268420 -2.7713537  1.0610354  1.1128789  1.0994356  0.88285796  1.05864136
13         NA          NA 0.6681936  1.1268420  1.1268420  1.1268420  1.0449097  1.12684196  1.12684196
14         NA          NA        NA  0.4605665  1.0052595  1.1153703  1.1131067  1.04581568  1.04490975
15         NA          NA        NA         NA  0.4654397 -1.3578072  1.1268420  0.95140180 -0.39118978
16         NA          NA        NA         NA         NA  0.6486259  1.1268420  0.71475592  1.01096175
17         NA          NA        NA         NA         NA         NA  0.7039338  1.06763729  1.12471067
18         NA          NA        NA         NA         NA         NA         NA  0.45755030  1.06456389
19         NA          NA        NA         NA         NA         NA         NA          NA  0.72025361
20         NA          NA        NA         NA         NA         NA         NA          NA          NA
21         NA          NA        NA         NA         NA         NA         NA          NA          NA
22         NA          NA        NA         NA         NA         NA         NA          NA          NA
          20        21       22
1  1.1268420 1.1268420 1.126842
2  1.1268420 1.1268420 1.126842
3  1.1268420 1.1268420 1.126842
4  1.1131067 1.1268420 1.126842
5  1.1067230 1.1268420 1.126842
6  1.1268420 1.1268420 1.126842
7  1.1067230 1.1268420 1.126842
8  1.1268420 1.1268420 1.126842
9  1.1067230 1.1268420 1.126842
10 1.1268420 1.1268420 1.126842
11 1.1268420 1.1268420 1.126842
12 1.1131067 1.1268420 1.126842
13 1.1268420 1.1268420 1.126842
14 1.1268420 1.1268420 1.126842
15 1.1067230 1.1268420 1.126842
16 1.1067230 1.1268420 1.126842
17 1.1268420 1.1268420 1.126842
18 1.1067230 1.1268420 1.126842
19 1.1067230 1.1268420 1.126842
20 0.8522286 0.6143475 1.126842
21        NA 0.8040364 1.126842
22        NA        NA 0.873158

$bootstrapping_results_walktrap_15
           1        2         3         4         5         6         7          8         9         10
1  0.5682761 0.878977 0.5429863 0.8651600 0.8635363 0.8789770 0.7992195  0.8618871 0.8789770  0.8246326
2         NA 1.029267 0.8789770 0.8635363 0.8789770 0.8789770 0.8500808  0.8789770 0.8789770  0.8789770
3         NA       NA 0.5716076 0.3421349 0.6618842 0.8789770 0.7825645  0.4592485 0.8635363  0.7477046
4         NA       NA        NA 0.4542557 0.8051221 0.8789770 0.7085440  0.1583161 0.8565861  0.8560689
5         NA       NA        NA        NA 0.5035466 0.8789770 0.8643556 -0.5066611 0.8789770  0.8639326
6         NA       NA        NA        NA        NA 0.9951257 0.8720097  0.8789770 0.8789770  0.8789770
7         NA       NA        NA        NA        NA        NA 0.8133522  0.8430914 0.8789770  0.8694777
8         NA       NA        NA        NA        NA        NA        NA  0.5405562 0.8740688  0.8386150
9         NA       NA        NA        NA        NA        NA        NA         NA 0.9509551 -0.3664340
10        NA       NA        NA        NA        NA        NA        NA         NA        NA  0.9724211
11        NA       NA        NA        NA        NA        NA        NA         NA        NA         NA
12        NA       NA        NA        NA        NA        NA        NA         NA        NA         NA
13        NA       NA        NA        NA        NA        NA        NA         NA        NA         NA
          11        12       13
1  0.8789770 0.8377270 0.878977
2  0.8789770 0.8789770 0.878977
3  0.8788002 0.5167107 0.878977
4  0.8785247 0.8196131 0.878977
5  0.8789770 0.8633355 0.878977
6  0.6735246 0.8789770 0.878977
7  0.6744351 0.8342063 0.878977
8  0.8789770 0.8453748 0.878977
9  0.8789770 0.8635363 0.878977
10 0.8789770 0.8654282 0.878977
11 1.0445582 0.8778154 0.878977
12        NA 0.9515792 0.878977
13        NA        NA 1.121023

$bootstrapping_results_walktrap_20
           1         2         3         4         5         6         7         8         9
1  0.5454626 0.9349825 0.9349825 0.9222283 0.3012490 0.5832378 0.9349825 0.9349825 0.9349825
2         NA 0.9708135 0.9349825 0.9313087 0.9275175 0.9349825 0.9349825 0.9349825 0.9349825
3         NA        NA 0.5923971 0.9229469 0.9221966 0.8785964 0.9349825 0.9349825 0.9349825
4         NA        NA        NA 0.6643224 0.5127162 0.8362766 0.9349825 0.9349825 0.6910755
5         NA        NA        NA        NA 0.4755791 0.1343549 0.9349825 0.9349825 0.9349825
6         NA        NA        NA        NA        NA 0.4728529 0.9124333 0.9349825 0.9343165
7         NA        NA        NA        NA        NA        NA 0.8841570 0.9349825 0.9349825
8         NA        NA        NA        NA        NA        NA        NA 0.9524640 0.6566124
9         NA        NA        NA        NA        NA        NA        NA        NA 0.8422199
10        NA        NA        NA        NA        NA        NA        NA        NA        NA
11        NA        NA        NA        NA        NA        NA        NA        NA        NA
12        NA        NA        NA        NA        NA        NA        NA        NA        NA
13        NA        NA        NA        NA        NA        NA        NA        NA        NA
            10           11        12        13
1   0.92219662 0.9307583564 0.9349825 0.9349825
2   0.93498254 0.9275174704 0.9349825 0.9057129
3   0.93498254 0.8482516468 0.9349825 0.9349825
4   0.73513585 0.6913207595 0.7887509 0.9349825
5   0.88615974 0.0007058748 0.9221966 0.9349825
6   0.02713836 0.8492805845 0.4970422 0.9349825
7  -0.74405019 0.9349825421 0.9349825 0.9349825
8   0.93498254 0.9349825421 0.9349825 0.9349825
9   0.91282403 0.9349825421 0.9349825 0.9349825
10  0.54399103 0.9234032415 0.8723314 0.9349825
11          NA 0.8000215869 0.9349825 0.9349825
12          NA           NA 0.9464180 0.9349825
13          NA           NA        NA 1.0650175

$bootstrapping_results_walktrap_25
          1        2         3         4         5         6         7        8
1 0.6401756 0.902586 0.8045481 0.8829504 0.8270410 0.7348924 0.8761060 0.758956
2        NA 0.797300 0.9025860 0.9025860 0.9025860 0.8454894 0.9025860 0.902586
3        NA       NA 0.5999639 0.8965087 0.5405041 0.8762362 0.8474989 0.902586
4        NA       NA        NA 0.6060054 0.6213154 0.4952407 0.9017369 0.902586
5        NA       NA        NA        NA 0.7222909 0.4400087 0.8125231 0.902586
6        NA       NA        NA        NA        NA 0.5778824 0.8759082 0.902586
7        NA       NA        NA        NA        NA        NA 0.9322287 0.902586
8        NA       NA        NA        NA        NA        NA        NA 1.044393

graph-based, louvain

louvain_bootstrapping_df <- plot_cluster_stability(sample_290_normalized, c(5:25), 5, "louvain")
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
louvain_bootstrapping_df
$bootstrapping_results_louvain_5
           1         2          3           4          5         6           7          8         9
1  0.1162653 0.5286774 0.49299852  0.39231136 0.65056808 0.7809545  0.43863738  0.5657062 0.7299181
2         NA 0.3267664 0.05846251  0.11821780 0.44696071 0.7809545  0.32600558  0.6658760 0.6941972
3         NA        NA 0.34192172 -0.08109674 0.62983914 0.7809545 -0.06834833  0.1321774 0.7729311
4         NA        NA         NA  0.46498547 0.04189229 0.7809545 -0.31113572 -0.4593382 0.7381432
5         NA        NA         NA          NA 0.18539616 0.7809545 -0.02501738  0.6573275 0.3634234
6         NA        NA         NA          NA         NA 1.2190455  0.78095451  0.7809545 0.7809545
7         NA        NA         NA          NA         NA        NA  0.29912611 -0.7252094 0.5290518
8         NA        NA         NA          NA         NA        NA          NA  0.4470762 0.7694778
9         NA        NA         NA          NA         NA        NA          NA         NA 0.2208099
10        NA        NA         NA          NA         NA        NA          NA         NA        NA
11        NA        NA         NA          NA         NA        NA          NA         NA        NA
12        NA        NA         NA          NA         NA        NA          NA         NA        NA
13        NA        NA         NA          NA         NA        NA          NA         NA        NA
14        NA        NA         NA          NA         NA        NA          NA         NA        NA
          10        11        12        13        14
1  0.7714659 0.7809545 0.7809545 0.7809545 0.7502048
2  0.7060206 0.7809545 0.7809545 0.7809545 0.7479405
3  0.7631415 0.7809545 0.7809545 0.7809545 0.6991967
4  0.6519251 0.7809205 0.7809545 0.7809545 0.5396857
5  0.6594438 0.7809545 0.7809545 0.7809545 0.6595305
6  0.7809545 0.7809545 0.7809545 0.7553386 0.7809545
7  0.7110823 0.7809545 0.7809545 0.7809545 0.6439248
8  0.6748801 0.7743755 0.7809545 0.7809545 0.6324611
9  0.6652328 0.7809545 0.7809545 0.7809545 0.7194283
10 0.1444341 0.7711004 0.7809545 0.7809545 0.7683622
11        NA 0.3161987 0.7809545 0.7809545 0.7232782
12        NA        NA 1.1056620 0.7809545 0.7809545
13        NA        NA        NA 0.6398171 0.7809545
14        NA        NA        NA        NA 0.1862816

$bootstrapping_results_louvain_10
           1          2         3         4          5            6         7           8         9
1  0.2473704 0.04570967  0.476384 0.6288087  0.8180017  0.610267010 1.0037662  0.86367833 0.9671207
2         NA 0.53319242 -1.599963 0.1258976  0.5872328  0.391256870 1.0037662  0.93837340 0.9196696
3         NA         NA  0.575916 0.1936520  0.8921062 -0.007416019 1.0051000  0.44577929 0.9487689
4         NA         NA        NA 0.3269078 -0.9793703 -0.378862234 1.0048897 -0.24018662 0.9151863
5         NA         NA        NA        NA  0.3033987  0.453110304 1.0294488  0.93477435 0.9028515
6         NA         NA        NA        NA         NA  0.563119320 1.0367463  0.04718961 0.9677154
7         NA         NA        NA        NA         NA           NA 0.7362361  1.01030714 1.0367463
8         NA         NA        NA        NA         NA           NA        NA  0.55667544 0.7891054
9         NA         NA        NA        NA         NA           NA        NA          NA 0.2855326
10        NA         NA        NA        NA         NA           NA        NA          NA        NA
11        NA         NA        NA        NA         NA           NA        NA          NA        NA
12        NA         NA        NA        NA         NA           NA        NA          NA        NA
13        NA         NA        NA        NA         NA           NA        NA          NA        NA
          10        11        12        13
1  0.9944210 1.0367463 0.9754163 1.0367463
2  0.9781032 1.0367463 1.0054463 1.0367463
3  1.0351450 1.0367463 0.9451158 1.0367463
4  0.7380862 1.0367463 0.7920203 1.0367463
5  0.5210447 1.0367463 0.9044781 1.0367463
6  1.0312233 1.0367463 0.7822222 1.0367463
7  1.0367463 1.0367463 1.0367463 1.0367463
8  1.0367463 1.0367463 0.8451361 1.0367463
9  0.8452047 1.0294488 0.9924787 1.0367463
10 0.3325847 1.0366978 0.9464834 1.0367463
11        NA 0.4695916 0.9096314 1.0367463
12        NA        NA 0.4017059 1.0367463
13        NA        NA        NA 0.9195688

$bootstrapping_results_louvain_15
           1         2         3          4         5           6           7         8         9
1  0.4215075 0.1725344 0.5990470  0.7581539 1.0175210  0.67674632  0.95484433 0.9760049 0.9850794
2         NA 0.4756992 0.3028639  0.7010759 1.0175210 -0.04953896  0.86754111 0.9635618 0.9955859
3         NA        NA 0.3037625 -0.9565882 1.0175210 -1.03164144 -0.36201473 0.8943603 0.7432303
4         NA        NA        NA  0.2658983 1.0175210  0.14390782  0.95102725 0.8933575 0.5268055
5         NA        NA        NA         NA 0.3786006  1.01487571  1.00291886 1.0175210 1.0175210
6         NA        NA        NA         NA        NA  0.54150116  0.03951335 0.9404799 1.0110055
7         NA        NA        NA         NA        NA          NA  0.72958120 0.8817742 1.0170150
8         NA        NA        NA         NA        NA          NA          NA 0.3084321 0.8985629
9         NA        NA        NA         NA        NA          NA          NA        NA 0.3043807
10        NA        NA        NA         NA        NA          NA          NA        NA        NA
11        NA        NA        NA         NA        NA          NA          NA        NA        NA
         10        11
1  1.017521 0.9755865
2  1.017521 0.9945886
3  1.017521 0.8317078
4  1.017521 0.8451054
5  1.017521 1.0175210
6  1.017521 0.7128626
7  1.017521 0.9539786
8  1.017521 1.0002172
9  1.017521 0.9339079
10 0.512719 0.9716798
11       NA 0.6121876

$bootstrapping_results_louvain_20
           1          2         3          4           5         6           7         8         9
1  0.4827849 -0.1341857 0.8641263  0.9260466  0.81251212 1.1529476  1.07789206 1.1340792 1.1059554
2         NA  0.3591579 0.3585899  0.6779199  0.04412644 1.1408084  0.83273584 1.1244941 1.1007839
3         NA         NA 0.3576969 -1.4642851 -1.23028917 1.1453437  0.05997225 0.9998965 0.9172268
4         NA         NA        NA  0.5149432  0.72879846 1.1529476  1.08155580 1.0319902 0.5969345
5         NA         NA        NA         NA  0.49598082 1.1313333 -1.09170760 1.0685807 1.1270578
6         NA         NA        NA         NA          NA 0.3639062  1.15294764 1.1529476 1.1529476
7         NA         NA        NA         NA          NA        NA  0.60886877 1.1027079 1.1498838
8         NA         NA        NA         NA          NA        NA          NA 0.4297201 1.0943584
9         NA         NA        NA         NA          NA        NA          NA        NA 0.3843897
10        NA         NA        NA         NA          NA        NA          NA        NA        NA
11        NA         NA        NA         NA          NA        NA          NA        NA        NA
          10        11
1  1.1529476 1.0862343
2  1.1529476 1.0523757
3  1.1529476 0.8274166
4  1.1507256 0.9700722
5  1.1527803 0.4612309
6  1.1529476 1.1459303
7  1.1527786 0.8232249
8  1.1529476 1.1332563
9  1.1495683 1.0380187
10 0.5273953 0.9533133
11        NA 0.4364729

$bootstrapping_results_louvain_25
           1          2         3          4          5         6           7         8         9
1  0.4934605 -0.7477598 0.7770286  0.9454290 1.17032134 1.2073541  0.79515562 1.2002801 1.1549619
2         NA  0.3342984 0.1778415  0.7068807 0.74517214 1.2033710 -0.05520674 1.1751720 1.1368279
3         NA         NA 0.3084289 -1.2580107 0.08279849 1.1900633 -1.16726563 0.8926730 1.0493183
4         NA         NA        NA  0.4900880 1.12826897 1.2073541  0.65064121 0.5331506 1.1369276
5         NA         NA        NA         NA 0.61969206 1.1900633 -1.86691572 1.2069953 1.0960606
6         NA         NA        NA         NA         NA 0.4784022  1.19006328 1.2073541 1.2073541
7         NA         NA        NA         NA         NA        NA  0.45300042 1.1881135 1.1090548
8         NA         NA        NA         NA         NA        NA          NA 0.4010123 1.1516553
9         NA         NA        NA         NA         NA        NA          NA        NA 0.5377174
10        NA         NA        NA         NA         NA        NA          NA        NA        NA
11        NA         NA        NA         NA         NA        NA          NA        NA        NA
          10        11
1  1.2073541 1.1705120
2  1.2073541 1.1200488
3  1.2073541 0.9403677
4  1.2059491 1.0728441
5  1.2052284 0.6890795
6  1.2073541 1.2073541
7  1.2073541 0.7388616
8  1.2073541 1.1124933
9  1.2073541 1.1917026
10 0.4711264 1.0125282
11        NA 0.4856809

Session info

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pheatmap_1.0.12             ggpubr_0.4.0                bluster_1.4.0               readr_2.1.1                
 [5] scater_1.22.0               ggplot2_3.3.5               scuttle_1.4.0               SingleCellExperiment_1.16.0
 [9] SummarizedExperiment_1.24.0 Biobase_2.54.0              GenomicRanges_1.46.1        GenomeInfoDb_1.30.0        
[13] IRanges_2.28.0              S4Vectors_0.32.3            BiocGenerics_0.40.0         MatrixGenerics_1.6.0       
[17] matrixStats_0.61.0          magrittr_2.0.1             

loaded via a namespace (and not attached):
 [1] bitops_1.0-7              RColorBrewer_1.1-2        rprojroot_2.0.2           tools_4.1.2              
 [5] backports_1.4.0           utf8_1.2.2                R6_2.5.1                  irlba_2.3.3              
 [9] vipor_0.4.5               DBI_1.1.1                 colorspace_2.0-2          nnet_7.3-16              
[13] withr_2.4.3               tidyselect_1.1.1          gridExtra_2.3             compiler_4.1.2           
[17] cli_3.1.0                 BiocNeighbors_1.12.0      DelayedArray_0.20.0       labeling_0.4.2           
[21] scales_1.1.1              stringr_1.4.0             digest_0.6.29             rmarkdown_2.11           
[25] XVector_0.34.0            pkgconfig_2.0.3           htmltools_0.5.2           sparseMatrixStats_1.6.0  
[29] fastmap_1.1.0             rlang_0.4.12              rstudioapi_0.13           DelayedMatrixStats_1.16.0
[33] farver_2.1.0              generics_0.1.1            BiocParallel_1.28.2       dplyr_1.0.7              
[37] car_3.0-12                RCurl_1.98-1.5            BiocSingular_1.10.0       modeltools_0.2-23        
[41] GenomeInfoDbData_1.2.7    Matrix_1.3-4              Rcpp_1.0.7                ggbeeswarm_0.6.0         
[45] munsell_0.5.0             fansi_0.5.0               abind_1.4-5               viridis_0.6.2            
[49] lifecycle_1.0.1           stringi_1.7.6             yaml_2.2.1                carData_3.0-4            
[53] zlibbioc_1.40.0           flexmix_2.3-17            grid_4.1.2                parallel_4.1.2           
[57] ggrepel_0.9.1             crayon_1.4.2              lattice_0.20-45           cowplot_1.1.1            
[61] beachmat_2.10.0           splines_4.1.2             hms_1.1.1                 knitr_1.36               
[65] pillar_1.6.4              optparse_1.7.1            igraph_1.2.9              ggsignif_0.6.3           
[69] ScaledMatrix_1.2.0        glue_1.5.1                evaluate_0.14             renv_0.14.0              
[73] vctrs_0.3.8               tzdb_0.2.0                getopt_1.20.3             gtable_0.3.0             
[77] purrr_0.3.4               tidyr_1.1.4               assertthat_0.2.1          xfun_0.28                
[81] rsvd_1.0.5                broom_0.7.10              miQC_1.2.0                rstatix_0.7.0            
[85] viridisLite_0.4.0         tibble_3.1.6              beeswarm_0.4.0            cluster_2.1.2            
[89] ellipsis_0.3.2            here_1.0.1               
---
title: "Clustering"
author: "Data Lab for ALSF"
date: "2022"
output:
  html_document:
    toc: yes
    df_print: paged
  html_notebook:
    toc: yes
    toc_float: yes
---

This notebook will begin looking at clustering methods on the expression of the genes in a single sample of the dataset of interest, from an unbiased approach.

## Set Up 

```{r}
# Load libraries
library(magrittr)
library(scater)
library(readr)
library(bluster)
library(ggpubr)
library(pheatmap)

# Set file paths
data_dir <- file.path("results", "Gawad_processed_data")

# Source custom functions script
source(file.path("utils", "clustering-functions.R"))
```

## Read in data

```{r}
sample_290_normalized <- read_rds(
  file.path(data_dir, "SCPCS000216", "SCPCL000290_miQC_downstream_processed_normalized_reduced_sce.rds"))
```

## Perform clustering

### k-means

```{r fig.height = 10.5}
# Perform k-means clustering
sample_290_normalized <- kmeans_clustering(
  sample_290_normalized,
  params_range = c(4:10),
  step_size = 1,
  check_stability = TRUE
)

# grab column names with clustering results
kmeans_cols <- grep("kmeans", colnames(colData(sample_290_normalized)))
kmeans_cluster_names <- colnames(colData(sample_290_normalized)[, kmeans_cols])

# Plot k-means
kmeans_plot_list <- kmeans_cluster_names %>%
  purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + 
               theme_bw()+
               theme(text = element_text(size = 22)))

cowplot::plot_grid(plotlist = kmeans_plot_list, ncol = 4)
```

### graph-based, walktrap

```{r fig.height = 9.5}
# Perform graph-based walktrap clustering
sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  params_range = c(5:25),
  step_size = 5,
  weighting_type = "rank",
  cluster_function = "walktrap",
  check_stability = TRUE
)

# grab column names with clustering results
walktrap_cols <- grep("walktrap", colnames(colData(sample_290_normalized)))
walktrap_cluster_names <- colnames(colData(sample_290_normalized)[, walktrap_cols])

# Plot
walktrap_plot_list <- walktrap_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + 
                theme_bw() +
                theme(text = element_text(size = 22)))

cowplot::plot_grid(plotlist = walktrap_plot_list, ncol = 3)
```

### graph-based, louvain

```{r fig.height = 8.5}
# Perform graph-based louvain clustering
sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  params_range = c(5:25),
  step_size = 5,
  weighting_type = "jaccard",
  cluster_function = "louvain",
  check_stability = TRUE
)

# grab column names with clustering results
louvain_cols <- grep("walktrap", colnames(colData(sample_290_normalized)))
louvain_cluster_names <- colnames(colData(sample_290_normalized)[, louvain_cols])

# Plot
louvain_plot_list <- louvain_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + 
                theme_bw() +
                theme(text = element_text(size = 22)))


cowplot::plot_grid(plotlist = louvain_plot_list, ncol = 3)
```

## Check cluster validity stats

### k-means

```{r fig.height = 20.5}
# Check the k-means cluster validity stats for each of the clusters and return
# stats in a data frame
kmeans_stats_df <- create_metadata_stats_df(sample_290_normalized, c(4:10), 1, "kmeans")

# Preview the results
head(kmeans_stats_df)

# Summarize the stats and return in a data frame
kmeans_summary_stats_df <- summarize_clustering_stats(kmeans_stats_df)

# Preview the summary results
head(kmeans_summary_stats_df)
```

#### purity plots

```{r fig.height=10, fig.width=15}
# Plot individual cluster purity stats
kmeans_purity_plots <- plot_cluster_purity(kmeans_stats_df)

kmeans_purity_plots
```

#### silhouette width plots

```{r fig.height=10, fig.width=15}
# Plot individual cluster silhouette width stats
kmeans_silhouette_plots <- plot_cluster_silhouette_width(kmeans_stats_df)

kmeans_silhouette_plots
```

### graph-based, walktrap

```{r fig.height = 15.5}
# Check the walktrap cluster validity stats for each of the clusters and return
# stats in a data frame
walktrap_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "walktrap")
  
# Preview the all stats results
head(walktrap_stats_df)

# Summarize the stats and return in a data frame
walktrap_summary_stats_df <- summarize_clustering_stats(walktrap_stats_df)

# Preview the summary results
head(walktrap_summary_stats_df)
```

#### purity plots

```{r fig.height=10, fig.width=15}
# Plot individual cluster purity stats
walktrap_purity_plots <- plot_cluster_purity(walktrap_stats_df)

walktrap_purity_plots
```

#### silhouette width plots

```{r fig.height=10, fig.width=15}
# Plot individual cluster silhouette width stats
walktrap_silhouette_plots <- plot_cluster_silhouette_width(walktrap_stats_df)

walktrap_silhouette_plots
```

### graph-based, louvain

```{r fig.height = 9.5}
# Check the louvain cluster validity stats for each of the clusters and return
# stats in a data frame
louvain_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "louvain")

# Preview the results
head(louvain_stats_df)

# Summarize the stats and return in a data frame
louvain_summary_stats_df <- summarize_clustering_stats(louvain_stats_df)

# Preview the summary results
head(louvain_summary_stats_df)
```

#### purity plots

```{r fig.height=10}
# Plot individual cluster purity stats
louvain_purity_plots <- plot_cluster_purity(louvain_stats_df)

louvain_purity_plots
```

#### silhouette width plots

```{r fig.height=10}
# Plot individual cluster silhouette width stats
louvain_silhouette_plots <- plot_cluster_silhouette_width(louvain_stats_df)

louvain_silhouette_plots
```

### Summary plots

```{r}
summary_stats_df_list <- list("walktrap" = walktrap_summary_stats_df,
                              "louvain" = louvain_summary_stats_df)

# purity summary plot
plot_avg_validity_stats(summary_stats_df_list, "avg_purity")

#silhouette width summary plot
plot_avg_validity_stats(summary_stats_df_list, "avg_width")
```

## Check cluster stability

### k-means

```{r}
# Check cluster stability
kmeans_bootstrapping_df <- plot_cluster_stability(sample_290_normalized, c(4:10), 1, "kmeans")
kmeans_bootstrapping_df
```

### graph-based, walktrap

```{r}
walktrap_bootstrapping_df <- plot_cluster_stability(sample_290_normalized, c(5:25), 5, "walktrap")
walktrap_bootstrapping_df
```

### graph-based, louvain

```{r}
louvain_bootstrapping_df <- plot_cluster_stability(sample_290_normalized, c(5:25), 5, "louvain")
louvain_bootstrapping_df
```

## Session info

```{r}
sessionInfo()
```
